Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Robert Hanson]

The reason I opted for /view/ instead of /download/ is that its header for
/download/ is

Content-Type: application/octet-stream


whereas with /view/ it is

Content-Type: text/plain;charset=UTF-8

This makes sense, as "download" initiates in the browser exactly that -- a
download (save to file). Whereas Jmol just needs to view it. It seemed
safer to me to pull it in as a text file than a byte stream.

Could be wrong about that.

Bob

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Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Otis Rothenberger]

Dave,

OK, I get it. That’s why it’s downloading via “download" when I just enter the 
url in my browser. After playing around a bit, I see that either works as a 
Jmol load command:

load http://files.rcsb.org/download/1xpb.pdb 

load http://files.rcsb.org/view/1xpb.pdb 

I did not know that. I thought that I still had to go after these things via 
proxy in Jmol.

load  http://www.rcsb.org/pdb/files/1xpb.pdb 
 does not work. That’s why I was 
confused. It does work via server proxy. Bottom Line: It looks like  
http://www.rcsb.org/pdb/files/1xpb.pdb  
is history!

Thanks.

Otis


http://files.rcsb.org/download/1xpb.pdb
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org

> On Apr 12, 2016, at 5:00 AM, Dave Howorth  wrote:
> 
> On 2016-04-12 04:16, Otis Rothenberger wrote:
>> Bob,
>> 
>> I have been using http://www.rcsb.org/pdb/files/1xpb.pdb
>>  server side for these files,
>> and missed the redirect to http://files.rcsb.org/view/1xpb.pdb. This
>> is going to a url path marked as view, as opposed
>> http://files.rcsb.org/download/1xpb.pdb
>>  , which indicates
>> download.
>> 
>> The above is obvious, but I’m curious about the latter. They are
>> doing something here that forces a no dialog download, at least with
>> Safari/Mac. Are they doing something funky with the Content-Type that
>> could be causing problems?
> 
> 
> $ wget http://www.rcsb.org/pdb/files/1xpb.pdb
> --09:54:35--  http://www.rcsb.org/pdb/files/1xpb.pdb
>=> `1xpb.pdb'
> Resolving www.rcsb.org... 128.6.70.10
> Connecting to www.rcsb.org|128.6.70.10|:80... connected.
> HTTP request sent, awaiting response... 301 Moved Permanently
> Location: http://files.rcsb.org/view/1xpb.pdb [following]
> --09:54:35--  http://files.rcsb.org/view/1xpb.pdb
>=> `1xpb.pdb'
> Resolving files.rcsb.org... 165.230.17.202
> Connecting to files.rcsb.org|165.230.17.202|:80... connected.
> HTTP request sent, awaiting response... 200 OK
> Length: unspecified [text/plain]
> 
> [ <=> ] 208,575   --.--K/s
> 
> 09:54:36 (41.92 MB/s) - `1xpb.pdb' saved [208575]
> 
> 
> $ wget http://files.rcsb.org/download/1xpb.pdb
> --09:59:03--  http://files.rcsb.org/download/1xpb.pdb
>=> `1xpb.pdb.1'
> Resolving files.rcsb.org... 165.230.17.202
> Connecting to files.rcsb.org|165.230.17.202|:80... connected.
> HTTP request sent, awaiting response... 200 OK
> Length: unspecified [application/octet-stream]
> 
> [ <=> ] 208,575   --.--K/s
> 
> 09:59:04 (47.78 MB/s) - `1xpb.pdb.1' saved [208575]
> 
> 
> So apparently view is text/plain
> whilst download is application/octet-stream
> 
> Cheers, Dave
> 
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Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Dave Howorth]

On 2016-04-12 04:16, Otis Rothenberger wrote:
> Bob,
>
> I have been using http://www.rcsb.org/pdb/files/1xpb.pdb
>  server side for these files,
> and missed the redirect to http://files.rcsb.org/view/1xpb.pdb. This
> is going to a url path marked as view, as opposed
> http://files.rcsb.org/download/1xpb.pdb
>  , which indicates
> download.
>
> The above is obvious, but I’m curious about the latter. They are
> doing something here that forces a no dialog download, at least with
> Safari/Mac. Are they doing something funky with the Content-Type that
> could be causing problems?


$ wget http://www.rcsb.org/pdb/files/1xpb.pdb
--09:54:35--  http://www.rcsb.org/pdb/files/1xpb.pdb
=> `1xpb.pdb'
Resolving www.rcsb.org... 128.6.70.10
Connecting to www.rcsb.org|128.6.70.10|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1xpb.pdb [following]
--09:54:35--  http://files.rcsb.org/view/1xpb.pdb
=> `1xpb.pdb'
Resolving files.rcsb.org... 165.230.17.202
Connecting to files.rcsb.org|165.230.17.202|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]

 [ <=> ] 208,575   --.--K/s

09:54:36 (41.92 MB/s) - `1xpb.pdb' saved [208575]


$ wget http://files.rcsb.org/download/1xpb.pdb
--09:59:03--  http://files.rcsb.org/download/1xpb.pdb
=> `1xpb.pdb.1'
Resolving files.rcsb.org... 165.230.17.202
Connecting to files.rcsb.org|165.230.17.202|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/octet-stream]

 [ <=> ] 208,575   --.--K/s

09:59:04 (47.78 MB/s) - `1xpb.pdb.1' saved [208575]


So apparently view is text/plain
whilst download is application/octet-stream

Cheers, Dave

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Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Otis Rothenberger]

Bob,

I have been using http://www.rcsb.org/pdb/files/1xpb.pdb 
 server side for these files, and 
missed the redirect to http://files.rcsb.org/view/1xpb.pdb. This is going to a 
url path marked as view, as opposed  http://files.rcsb.org/download/1xpb.pdb 
 , which indicates download.

The above is obvious, but I’m curious about the latter. They are doing 
something here that forces a no dialog download, at least with Safari/Mac. Are 
they doing something funky with the Content-Type that could be causing problems?

Otis

--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org

> On Apr 11, 2016, at 7:18 PM, Robert Hanson  wrote:
> 
> Hmm. That was supposed to read:
> 
> I notice that http://www.rcsb.org/pdb/files/1xpb.pdb 
>  is giving a 301 move-permanently 
> redirect. It's possible that Firefox can handle that in AJAX but Chrome 
> cannot. These are getting re-directed to 
> http://files.rcsb.org/download/1xpb.pdb 
> 
> 
> ps - there is no need to use .gz. You only make trouble for JSmol doing that. 
> 
> I have just uploaded http://chemapps.stolaf.edu/jmol/jsmol/JSmol.min.js 
>  again with an addition 
> to allow specifying .gz for those files as well. The  file will NOT be 
> transferred as gz, though.
> 
> Bob
> 
> ​
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Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Robert Hanson]

Hmm. That was supposed to read:

I notice that http://www.rcsb.org/pdb/files/1xpb.pdb is giving a 301
move-permanently redirect. It's possible that Firefox can handle that in
AJAX but Chrome cannot. These are getting re-directed to
http://files.rcsb.org/download/1xpb.pdb

ps - there is no need to use .gz. You only make trouble for JSmol doing
that.

I have just uploaded http://chemapps.stolaf.edu/jmol/jsmol/JSmol.min.js
again with an addition to allow specifying .gz for those files as well.
The  file will NOT be transferred as gz, though.

Bob

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Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Robert Hanson]

I notice that http://www.rcsb.org/pdb/files/1xpb.pdb is giving a 301
move-permanently redirect. It's possible that Firefox can handle that in
AJAX but Chrome cannot. These are getting re-directed to
http://www.rcsb.org/pdb/files/1xpb.pdb

I have added into JSmol the capability of automatically doing that switch.
If you need this fast, see
http://chemapps.stolaf.edu/jmol/jsmol/JSmol.min.js,  which  I have just now
updated.

Bob​
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Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Luciano Abriata]

Dear Rolf and Angel,
Using the version that Rolf pointed out and cleaning the caches worked on all 
my tests (chrome in windows 8, linux centos 6 and mac not sure which OS). 
Refreshing the page is not enough, you really need to clear the cache.
Thanks to both of you!
Luciano




  De: Angel Herráez 
 Para: jmol-users@lists.sourceforge.net 
 Enviado: Lunes, 11 de abril, 2016 16:58:00
 Asunto: Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work
   
Luciano, it may be what Rolf is saying. However, given that it is 
browser-specific, I think it is something different.

SInce you are asking to load binary files (gzipped), there is a need for JSmol 
in some browsers to use the jsmol.php file as an intermediary.
Maybe you haven't that properly configured in your pages

See  
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Reading_binary_files
and particularly the use of "serverURL",
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Files_and_paths

or send us one of your URL to check what is happening

·
 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28871 Alcalá de Henares  (Madrid), Spain


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Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Angel Herráez]

Luciano, it may be what Rolf is saying. However, given that it is 
browser-specific, I think it is something different.

SInce you are asking to load binary files (gzipped), there is a need for JSmol 
in some browsers to use the jsmol.php file as an intermediary.
Maybe you haven't that properly configured in your pages

See  
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Reading_binary_files
and particularly the use of "serverURL",
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Files_and_paths

or send us one of your URL to check what is happening

·
 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28871 Alcalá de Henares  (Madrid), Spain


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Re: [Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Rolf Huehne]

On 04/11/2016 02:27 PM, Luciano Abriata wrote:
> Hello,
> I am having a strange problem. If visited from Chrome, my website cannot 
> retrieve PDB files from the PDB (load command), neither from the server nor 
> locally.
> However... it does work in Firefox, it did work in Chrome at least 1-2 months 
> ago, and last, I see other JSmol sites working ok in Chrome. The latter fact 
> makes me think I did something dirty that saw the light now because of some 
> update at the PDB or Chrome... (BTW, I have this problem with old and with 
> the latest JSmol versions).
> In the canvas HTML object in Chrome, the load command gives me:
> Unrecognized file format for filehttp://www.rcsb.org/pdb/files/1xpb.pdb.gz  
> (example)
> NetworkError: Failed to execute 'send' on 'XMLHttpRequest': Failed to load 
> 'http://www.rcsb.org/pdb/files/1xpb.pdb.gz'
>
>
>
> Any ideas what the problem could be, or what I should pay attention to?
> Many many thanks!
> Luciano
Luciano, it looks like a problem that was solved recently and discussed 
on this list a few weeks ago "[Jmol-users] New path for RCSB files 
causes Jmol error" (see 
"https://sourceforge.net/p/jmol/mailman/message/34960913/";).

According to this you need Jmol version 14.4.4_2016.03.24 or above. If 
you already have installed this version there might be a caching problem 
and files from an earlier version might interfere with the newer 
version. In this case you should empty the browser cache, restart the 
browser, and try again.

Since there can be released several new bug fix versions within a few 
days the term 'latest versions' is not a good choice. It is always 
better to provide the exact version number(s) in a help request.

Regards,
Rolf

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[Jmol-users] Cannot load PDBs from RCSB in Chrome -used to work

[Luciano Abriata]

Hello,
I am having a strange problem. If visited from Chrome, my website cannot 
retrieve PDB files from the PDB (load command), neither from the server nor 
locally.
However... it does work in Firefox, it did work in Chrome at least 1-2 months 
ago, and last, I see other JSmol sites working ok in Chrome. The latter fact 
makes me think I did something dirty that saw the light now because of some 
update at the PDB or Chrome... (BTW, I have this problem with old and with the 
latest JSmol versions).
In the canvas HTML object in Chrome, the load command gives me:
Unrecognized file format for filehttp://www.rcsb.org/pdb/files/1xpb.pdb.gz  
(example)
NetworkError: Failed to execute 'send' on 'XMLHttpRequest': Failed to load 
'http://www.rcsb.org/pdb/files/1xpb.pdb.gz'



Any ideas what the problem could be, or what I should pay attention to?
Many many thanks!
Luciano
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